Abstract:
In this work we introduce a graph theoretical method to
compare MEPs, which is independent of molecular
alignment. It is based on the edit distance of weighted rooted
trees, which encode the geometrical and
topological information of Negative Molecular Isopotential
Surfaces. A meaningful chemical classification
of a set of 46 molecules with different functional groups was
achieved. Structure-activity relationships for
the corticosteroid binding affinity (CBG) of 31 steroids by
means of hierarchical clustering resulted in a
clear partitioning in high, intermediate, and low activity
groups, whereas the results from quantitative
structure-activity relationships, obtained from a partial
least-squares analysis, showed comparable or better
cross-validated correlation coefficients than the ones
reported for previous methods based solely in the
MEP.
Characterization of Activity Landscapes Using
2D and 3D Similarity Methods: Consensus Activity Cliffs
J.
Chem. Inf. Model. 2009, 49, 2, 477-491
Jose L. Medina-Franco, Karina Martínez-Mayorga, Andreas
Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia
Pinilla, Richard A. Houghten
Abstract:
Activity landscape characterization has been demonstrated to
be a valuable tool in lead optimization, virtual screening,
and computational modeling of active compounds. In this work,
we present a general protocol to explore systematically the
activity landscape of a lead series using 11 2D and 3D
structural representations. As a test case we employed a set
of 48 bicyclic guanidines (BCGs) with κ-opioid receptor
binding affinity, identified in our group. MACCS keys,
graph-based three point pharmacophores, circular fingerprints,
ROCS shape descriptors, and the TARIS approach, that compares
structures based on molecular electrostatic potentials, were
employed as orthogonal descriptors. Based on ‘activity cliffs’
common to a series of descriptors, we introduce the concept of
consensus activity cliffs. Results for the current test case
suggest that the presence or absence of a methoxybenzyl group
may lead to different modes of binding for the active BCGs
with the κ-opioid receptor. The most active compound (IC50 =
37 nM) is involved in a number of consensus cliffs making it a
more challenge query for future virtual screening than would
be expected from affinity alone. Results also reveal the
importance of screening high density combinatorial libraries,
especially in the “cliff-rich” regions of activity landscapes.
The protocol presented here can be applied to other data sets
to develop a consensus model of the activity landscape.
Parallel Computing System for the efficient
calculation of molecular similarity based on
negative electrostatic potential
Raul E. Torres
Master's
Thesis, Universidad Nacional de Colombia
Abstract:
This document proposes an alternative method for
the comparison of molecular electrostatic potential (MEP),
based on parallel computing algorithms on graphics cards using
NVIDIA CUDA platform and kernel methods for pattern
recognition. The proposed solution optimizes the construction
process of a particular representation of MEP, presents
options for improving this representation, and offers 11
kernel functions for comparison process. Experimental
evaluation using cluster analysis shows good results on a set
of 73 molecules from classic chemistry functional groups,
finding relationships of acidity and basicity using edit
distance and detecting presence of oxygen, nitrogen and
functional groups (C=O or C-O) when kernel functions are used.